[Biojava-l] Cookbook entry - feedback please

[Andreas Prlic]

> A question concerning consensus sequences: how do you handle gaps? N
> (as I understood it) does not allow a gap. Is there a way to encode a
> "might be gap here, or A or G"?

If the input is a multiple sequence alignment then you could count
frequencies at each position and take the most frequently occurring
nucleotide. For each position you could count a conservation score.

Andreas